长非编码RNA研究进展

长非编码RNA是指一类长度大于200个核苷酸、不编码蛋白质的非编码RNA.越来越多的研究表明,人类基因组中高达90%的非编码蛋白质的区段同样具有重要作用,而不是所谓的"转录噪声".针对长非编码RNA的功能研究表明,其在转录起始的调控、转录及转录后的调控中均发挥着重要作用,因而影响着各种各样的生物学过程.本综述围绕近几年长非编码RNA的研究成果,总结了长非编码RNA的起源与进化、新型的长非编码RNA类型、典型的长非编码RNA作用机制以及长非编码RNA在发育与细胞重编程过程中的研究,同时也概述了长非编码RNA与表观遗传调控和癌症的关系以及长非编码RNA研究的相关技术.系统发现长非编码RNA并阐明其功能机制,将对现代生命科学具有重大的意义.     

非编码RNA功能与功能机理研究

真核生物基因组具有广泛转录的特性,其中绝大部分转录产物为不编码蛋白质的非编码RNA.这些非编码RNA又可分为长链非编码RNA和小非编码RNA,并且两者都行使重要的调控功能.同时,非编码RNA也被用作生物技术及应用于生物医学.本文就非编码RNA在动物细胞基因表达等重要生命事件中的功能及功能机理进行综述,并简要介绍非编码RNA相关的生物技术、生物医学应用.     

非编码RNA与代谢的研究进展

非编码RNA是指不编码蛋白质的调节性RNA分子.近年来的研究发现,非编码RNA,尤其是微小RNA和长非编码RNA,可以在基因转录、RNA成熟和蛋白质翻译等水平调控基因表达,参与发育、分化和新陈代谢等几乎所有重要的生理生命过程,在人类疾病中发挥重要作用.肿瘤和糖尿病等代谢性疾病是人类健康和社会发展的重大威胁.代谢紊乱是肿瘤的主要特征之一.胰岛素抵抗是糖尿病发生发展的主要因素,它与胰岛素产生和分泌以及胰岛素信号通路密切相关.本文将从非编码RNA的产生和作用机制、非编码RNA与胰岛素信号通路及糖尿病、非编码RNA与肿瘤代谢等方面,对非编码RNA在代谢领域的研究进展进行综述.     

nc2Cancer:一个研究与癌症相关人类非编码RNA的数据库

伴随着高通量测序技术的飞速发展,许多新型的非编码RNA陆续被发现,比如长链非编码RNA(lncRNA)和环状RNA(Circular RNA)。先前的研究已经表明这些非编码RNA在基因表达调控过程中起着很重要的作用,并且与癌症的发生有着很密切的联系。但是,由于研究者们仍然对它们行使何种功能知之甚少,鉴定这些非编码RNA是否与人类癌症存在密切的相互关系仍然是一个巨大的挑战。为了促进这一领域的研究,这篇文章的作者分析了大规模的RNA相互作用数据,然后建立了数据库nc2Cancer(http://www.bioinfo.tsinghua.edu.cn/nc2Cancer/index.php)。这个数据库的目标便是提供非编码RNA与癌症之间的全面关系。现在,该nc2Cancer数据库包括了三种类型的非编码RNA分子:长链非编码RNA,环状RNA以及由假基因转录而成的RNA。这项研究将有助于研究者更好地去理解非编码RNA的功能以及它们在人类癌症发生过程中所起到的作用。     

非编码RNA研究进展

非编码RNA是指不具备蛋白质编码能力的RNA,包括转运RNA、核糖体RNA、小核仁RNA(small nucleolar RNA, snoRNA)以及长非编码RNA(long noncoding RNA, lncRNA)等.非编码RNA广泛参与生命活动中重要的生物功能,如生物个体的发育与分化、生殖、细胞凋亡和细胞重编程等,并且与人类疾病密切相关.近年来,随着我国经济的发展和人口老龄化,心血管疾病、肿瘤、代谢性疾病等疾病已成为威胁中国居民健康的重大慢性非传染性疾病,一些罕见病,例如小胖威利综合征(Prader-Willi syndrome, PWS)也随着人口基数的不断增大逐渐影响我国居民的身体健康.随着对这些慢性疾病及罕见疾病发生发展的相关机制研究,我国科学家发现非编码RNA与这些疾病密切相关.非编码RNA参与调控一系列的心血管疾病、肿瘤、代谢性疾病、感染免疫性疾病和PWS等疾病过程.本文对我国学者在非编码RNA领域的贡献进行综述,详细阐述了非编码RNA的加工形成和功能研究等主要进展,并对探究这些非编码RNA与PWS、心血管疾病、肿瘤、代谢性疾病和感染免疫性疾病等发生发展中的重要调控作用,以及我国科学家对该领域的贡献进行了详细的综述和总结.     

利用转录组数据鉴定和分析小鼠非编码RNA

基因转录表达是一个复杂、精确并具有时空特异性的过程.目前对转录组的研究主要集中在蛋白编码基因上.近几年,一个新的转录组研究工具—大规模并行c DNA测序技术(RNA-seq)为更深入地研究转录组带来了希望.利用RNA-seq数据,鉴定出大量的非编码RNA,特别是lincRNA,并且发现这些非编码RNA是多个生物学过程中重要的调控因子.利用深度测序获得的15个小鼠组织RNA-seq数据探索非编码RNA在小鼠不同组织中的多样性和动态变化.依据自定的标准,在这15个组织中共鉴定出16249个非编码基因(对应21569个非编码RNA).研究这些非编码RNA的多种特征,可以发现与蛋白编码基因相比,非编码RNA通常比较短,外显子个数少,表达量低,组织特异性强.而且,这些非编码RNA有明显的转录起始和转录延伸信号(H3K4me3,H3K27me3,H3K36me3修饰,RNAPⅡ结合位点以及CAGE)的富集.基因集富集分析结果表明,lincRNA与多个生物学过程相关,如免疫反应、肌肉发育和有性生殖等.本研究提供了更加全面的对小鼠非编码RNA的注释信息,为小鼠非编码RNA的功能和进化研究奠定了基础.     

miRNA,lncRNA与心血管疾病

近年来,心血管疾病在我国的发病率和致死率呈逐年上升趋势,已成为威胁我国公众健康的重要疾病之一.尽管长期的研究使人们对心血管疾病有了一定的了解,但是其发病机制尚未完全清楚.非编码RNA(non-coding RNA,ncRNA)是指转录组中不编码蛋白的功能性RNA分子,包括微小RNA(microRNA,miRNA)和长链非编码RNA(long non-coding RNA,lncRNA)等.miRNA是一类在进化上高度保守,具有转录后调节活性的单链非编码小分子RNA.而lncRNA是一类转录本长度超过200个核苷酸的功能性非编码RNA分子.研究表明,这些功能性ncRNA不但在细胞增殖、分化和衰老过程中发挥着重要作用,还参与了癌症、神经退行性疾病和心血管疾病等疾病的病理进程.本文将着重概述miRNA和lncRNA在心血管疾病中的作用及其最新研究进展.     

长链内含子非编码RNA在基因表达过程中的调控作用

在绝大多数人类基因中都存有非蛋白编码RNA（non-coding RNA,ncRNA）.长链内含子ncRNA（long intronic non-coding RNA,lincRNA）是众多ncRNA中的一员,而内含子区域则是具有调节性的ncRNA的关键源.长链内含子ncRNA可通过作为短链RNA的前体、或是与启动子元件的交互作用、组蛋白甲基化修饰、蛋白编码RNA选择性剪接以及蛋白质编码RNA的稳定性,从而对基因表达进行调控.至此我们可以逐步揭示出基于长链内含子ncRNA的调控系统模式.     

小RNA介导组蛋白3赖氨酸27的三甲基化(H3K27me3)

<正>生物体内存在大量的不编码蛋白质序列的非编码RNA(noncoding RNA,nc RNA),这些非编码RNA广泛参与生命活动的各个过程,包括基因表达调控、基因组稳定性维持、抵抗外源核酸侵染、个体生长发育和生殖等生理过程以及肿瘤发生等病理过程.在真核生物中,长双链RNA(double-stranded RNA,ds RNA)被摄取到细胞内后,首先被一类保守性     

缺氧相关长链非编码RNA作为肝癌预后预测标志物的潜在价值

肝细胞癌(hepatocellular carcinoma,简称肝癌)是一种常见的恶性肿瘤。缺氧是肝癌等实体肿瘤的一个重要特征,同时也是诱导肿瘤恶性进展的重要因素。然而,肝癌缺氧相关的长链非编码RNA(long non-coding RNA,lncRNA)的鉴定及其在临床生存预后等方面的价值仍未得到系统的研究。本研究旨在通过肝癌转录组的整合分析鉴定肝癌缺氧相关的lncRNA,并评估其在肝癌预后中的价值。基于癌症基因组图谱(The Cancer Genome Atlas,TCGA)计划的肝癌转录组数据的整合分析,初步鉴定到233个缺氧相关的候选lncRNA。进一步筛选具有预后价值的候选者,基于其中12个缺氧相关lncRNA(AC012676.1、PRR7-AS1、AC020915.2、AC008622.2、AC026401.3、MAPKAPK5-AS1、MYG1-AS1、AC015908.3、AC009275.1、MIR210HG、CYTOR和SNHG3)建立了肝癌预后风险模型。Cox比例风险回归分析显示,基于该模型计算的缺氧风险评分作为肝癌患者新的独立预后预测指标,优于传统的临床病理因...     

Expression of stathmin family genes in the murine uterus during early pregnancy

Stathmin, a cytosolic phosphoprotein that regulates microtubule dynamics during cell-cycle progression, is abundantly expressed at embryo implantation sites in rats. Here, we characterized the expression of stathmin and its family genes in the murine uterus during the peri-implantation period. Stathmin protein was expressed in the glandular and luminal epithelium, blood vessels, and stromal cells on day 3 of pregnancy. On the day of implantation (day 5), stathmin was mainly localized in blood vessels in the endometrium. On day 7, intense stathmin expression was limited to capillary vessels and secondary decidual cells. Stathmin expression was higher at implantation sites than at uterine segments between implantation sites and increased during oil-induced decidualization. Although the artificially-induced deciduoma weights and number of implantation sites were similar between stathmin-knockout (KO) and wild-type (WT) mice, the stathmin-KO mice had fewer newborn pups (reduced by 30%). The expression of alkaline phosphatase, desmin, and cyclin D3 was attenuated in decidual zones of stathmin-KO mice. Messenger RNA level of the stathmin family gene, SCG10, was high at the time of decidualization in WT and stathmin-KO mice. In contrast, the others of stathmin family members, SCLIP and RB3 were highly expressed in stathmin-KO mice compared to WT mice. These results suggest that stathmin and stathmin family genes are expressed in the murine endometrium with enhanced expression in the implantation or the decidualization process.     

Progesterone and DNA damage encourage uterine cell proliferation and decidualization through up-regulating ribonucleotide reductase 2 expression during early pregnancy in mice

Embryo implantation into the maternal uterus is a crucial step for the successful establishment of mammalian pregnancy. Following the attachment of embryo to the uterine luminal epithelium, uterine stromal cells undergo steroid hormone-dependent decidualization, which is characterized by stromal cell proliferation and differentiation. The mechanisms underlying steroid hormone-induced stromal cell proliferation and differentiation during decidualization are still poorly understood. Ribonucleotide reductase, consisting of two subunits (RRM1 and RRM2), is a rate-limiting enzyme in deoxynucleotide production for DNA synthesis and plays an important role in cell proliferation and tumorgenicity. Based on our microarray analysis, Rrm2 expression was significantly higher at implantation sites compared with interimplantation sites in mouse uterus. However, the expression, regulation, and function of RRM2 in mouse uterus during embryo implantation and decidualization are still unknown. Here we show that although both RRM1 and RRM2 expression are markedly induced in mouse uterine stromal cells undergoing decidualization, only RRM2 is regulated by progesterone, a key regulator of decidualization. Further studies showed that the induction of progesterone on RRM2 expression in stromal cells is mediated by the AKT/c-MYC pathway. RRM2 can also be induced by replication stress and DNA damage during decidualization through the ATR/ATM-CHK1-E2F1 pathway. The weight of implantation sites and deciduoma was effectively reduced by specific inhibitors for RRM2. The expression of decidual/trophoblast prolactin-related protein (Dtprp), a reliable marker for decidualization in mice, was significantly reduced in deciduoma and steroid-induced decidual cells after HU treatment. Therefore, RRM2 may be an important effector of progesterone signaling to induce cell proliferation and decidualization in mouse uterus.     

Ubiquitin-specific protease 7 (USP7) is essential for endometrial stromal cell decidualization in mice

Ubiquitin-specific protease 7 (USP7), a member of the deubiquitinating (DUB) enzyme family, regulates protein stability and has a well-characterized function in tumorigenesis. Given its critical role in growth and development, it was speculated to be involved in modulating processes in the female reproductive system but its exact role has not been elucidated. Decidualization is one of the key processes in pregnancy and aberrant decidualization is a cause of pregnancy failure. The uterine endometrium layer undergoes significant structural and functional changes during decidualization in preparation for and after embryo implantation. Here, we hypothesized that USP7 could be involved in mediating endometrial stromal cell (ESC) decidualization and set out to determine its function with a primary stromal cell culture. Using in situ hybridization and immunohistochemical techniques, we observed increased USP7 expression during uterine decidualization and found that it was predominantly localized to the decidual zone in the post-implantation uterus. Since the ovarian hormones, progesterone (P4) and estrogen (E2), function in promoting stroma decidualization, we investigated their relationship with USP7 expression and found that they exert minimal influence. Moreover, increased USP7 expression observed during deciduoma development was found to be independent of blastocyst attachment. Using a specific USP7 inhibitor, HBX19818, we demonstrated an additional novel role for USP7 in endometrial stroma decidualization in mice during early pregnancy. Our findings could potentially be applied towards future research and development in female infertility.     

Gamma‐amino butyric acid and the A‐type receptor suppress decidualization of mouse uterine stromal cells by down‐regulating cyclin D3

Uterine decidualization, characterized by stromal cell proliferation and differentiation into polyploid decidual cells, is critical to the establishment of pregnancy in mice, although the mechanism underlying this process remains poorly understood. This study is the first to investigate the expression of gamma‐amino butyric acid (GABA) and the GABA A‐type receptor π subunit (GABPR) in the early‐pregnancy mouse uterus and their roles in decidualization. The expression of GABRP was detected from Day 4 to 8 of pregnancy. The effects of GABA and GABA A‐type receptor on cell proliferation and apoptosis were investigated using the Cell Titer 96® AQueous One Solution Cell Proliferation Assay and flow cytometry. The levels of cyclin D3 protein were measured in cultured stromal cells artificially induced to undergo decidualization, and treated with GABA and a GABA A‐type receptor agonist or antagonist, respectively, at the same time. mRNA expression of gabrp in implantation sites was lower than that in inter‐implanted sites. GABA and GABRP protein were localized in the luminal and glandular epithelium, stromal cells, and decidual cells. In vitro, GABPR protein level was decreased in cultured stromal cells during the decidualization process. The addition of GABA and the GABA A‐type receptor agonist Muscimol inhibited stromal cell proliferation, promoted apoptosis, and arrested cells in S‐phase, followed by decreased expression of cyclin D3. These results show that in mice, GABA was actively involved in inhibiting stromal cell proliferation and suppresses decidualization progress through GABA A‐type receptors by down‐regulating cyclin D3 level. Mol. Reprod. Dev. 80: 59–69, 2013. © 2012 Wiley Periodicals, Inc.     

Maternal pentraxin 3 deficiency compromises implantation in mice

Reduced litter sizes in mice missing pentraxin 3 (Ptx3) have been attributed to fertilization failure. However, our global gene expression studies showed high uterine Ptx3 expression at the implantation site in mice, suggesting its role in blastocyst implantation. We initiated molecular and genetic studies in mice to explore the importance of uterine Ptx3 in this process. We found that Ptx3 is expressed in a unique and transient fashion at implantation sites. With the initiation of implantation on midnight of Day 4 of pregnancy, Ptx3 is expressed exclusively in stromal cells at the site of blastocysts. On Day 5, its expression is more intense in decidualizing stromal cells, but it disappears on Day 6. The expression again becomes evident in the deciduum on Day 7, followed by a more robust expression on Day 8, particularly at the antimesometrial pole. From Day 9, with the initiation of placentation, Ptx3 expression becomes undetectable. These results suggest a role for PTX3 in implantation and decidualization. Indeed, deletion of Ptx3 results in both compromised implantation and decidualization. Interleukin 1B (IL1B), a known inducer of Ptx3, is also transiently expressed in stromal cells at the implantation site, suggesting that IL1B is an inducer of uterine Ptx3 expression. In fact, uterine Ptx3 expression follows that of Il1b induced by lipopolysaccharide treatment on Day 7 of pregnancy. Collectively, these findings provide evidence for an important role for PTX3 in implantation and decidualization. This study has clinical implications, since PTX3 is expressed in the receptive endometrium, and trophoblast cells influence decidual Ptx3 expression in humans.     

Expression and Function of Kisspeptin during Mouse Decidualization

Background

Plasma kisspeptin levels dramatically increased during the first trimester of human pregnancy, which is similar to pregnancy specific glycoprotein-human chorionic gonadotropin. However, its particular role in the implantation and decidualization has not been fully unraveled. Here, the study was conducted to investigate the expression and function of kisspeptin in mouse uterus during early pregnancy and decidualization.

Methodology/Principal Findings

Quantitative PCR results demonstrated that Kiss1 and GPR54 mRNA levels showed dynamic increase in the mouse uterus during early pregnancy and artificially induced decidualization in vivo. KISS-1 and GPR54 proteins were spatiotemporally expressed in decidualizing stromal cells in intact pregnant females, as well as in pseudopregnant mice undergoing artificially induced decidualization. In the ovariectomized mouse uterus, the expression of Kiss1 mRNA was upregulated after progesterone or/and estradiol treatment. Moreover, in a stromal cell culture model, the expression of Kiss1 and GPR54 mRNA gradually rise with the progression of stromal cell decidualization, whereas the attenuated expression of Kiss1 using small interfering RNA approaches significantly blocked the progression of stromal cell decidualization.

Conclusion

our results demonstrated that Kiss1/GPR54 system was involved in promoting uterine decidualization during early pregnancy in mice.     

Expression of matrix metalloproteinases 2 and 9 in the mouse uterus during implantation and oil-induced decidualization

During implantation, matrix metalloproteinases are believed to play roles in the tissue remodelling that accompanies decidualization in the endometrium and in embryo invasion. The objective of this study was to characterize further the expression of matrix metalloproteinases 2 and 9 in the mouse uterus during early pregnancy and oil-induced decidualization. mRNA encoding matrix metalloproteinase 2 was detected in pregnant uteri and uteri undergoing oil-induced decidualization by northern blot analyses. The steady-state concentrations of mRNA encoding matrix metalloproteinase 2 did not change significantly in implantation compared with inter-implantation areas on days 5-8 of pregnancy but were significantly lower in stimulated compared with non-stimulated uterine horns during artificially induced decidualization. mRNA encoding matrix metalloproteinase 9 was also detected in uteri undergoing oil-induced decidualization but not in pregnant uteri. Its concentration was significantly greater in uterine horns undergoing oil-induced decidualization compared with control horns. Immunoreactive matrix metalloproteinases 2 and 9 were detected in the uterus during early pregnancy and oil-induced decidualization by immunohistochemistry, localized to the endometrial stroma, but the staining progressively became weaker and was absent in areas that had undergone decidualization. By day 8 of pregnancy and 72 h after the induction of decidualization, matrix metalloproteinase 2 and 9 proteins remained mainly in the region of non-decidualized stromal cells adjacent to the myometrium. In implantation segments, they were also localized to the region of the trophoblast giant cells. The second objective of the present study was to determine whether endometrial stromal cells isolated from uteri sensitized for decidualization express matrix metalloproteinases 2 and 9. Northern blot analyses and gelatin zymography showed that these cultured cells expressed matrix metalloproteinase 2 and 9, and that transforming growth factor beta1 significantly increased matrix metalloproteinase 9 expression. The results of the present study further characterize matrix metalloproteinases 2 and 9 expression in the uterus during implantation and artificially induced decidualization.     

Adam12 plays a role during uterine decidualization in mice

In mouse, decidualization is characterized by the proliferation of stromal cells and their differentiation into specialized type of cells (decidual cells) with polyploidy, surrounding the implanting blastocyst. However, the mechanisms involved in these processes remain poorly understood. Using multiple approaches, we have examined the role of Adam12 in decidualization during early pregnancy in mice. Adam12 is spatiotemporally expressed in decidualizing stromal cells in intact pregnant females and in pseudopregnant mice undergoing artificially induced decidualization. In the ovariectomized mouse uterus, the expression of Adam12 is upregulated after progesterone treatment, which is primarily mediated by nuclear progesterone receptor. In a stromal cell culture model, the expression of Adam12 gradually rises with the progression of stromal decidualization, whereas the attenuated expression of Adam12 after siRNA knockdown significantly blocks the progression of decidualization. Our study suggests that Adam12 is involved in promoting uterine decidualization during pregnancy.